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Re: [ccp4bb] Validate tool pdb structure
 

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CCP4bb <-- 2007 <-- March 2007 <-- 20 March 2007
Previous message:
Subject: Re: coot and stereochemistry
From: Dale Tronrud det102 {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2007-03-20 		Next message:
Subject: ccp4i error on Mac OS
From: Ulrich Genick genick {- at -} BRANDEIS {- dot -} EDU
Date: 2007-03-20


Subject: Re: Validate tool pdb structure
From: "Ibrahim M {- dot -} Moustafa" I {- dot -} moustafa {- at -} PSU {- dot -} EDU
Date: 2007-03-20
Actually, the structure is not mine. I just wanted to check the
structure before using it for my work!

The unit of the structure is: a = 141.59, b = 141.59, c = 43.68
alpha = 90.00, beta = 90.00, gamma = 120.00

So, it is H3 not R3!

Checking the structure after editing the space group to H3 did not
show any bad close contacts vs. R3 spg.

thanks for those who replied.

Ibrahim




At 01:50 PM 3/20/2007, henrick@ebi.ac.uk wrote:
>are you mixing R3 with H3 ?
>
>in the current pdb R3 has a=b=c, al=be=ga
> while H3 has a=b, al=90, be=90, ga=120
>this was not consistently used in the earlier pdb
>
>examples
>
>REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
>REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: R 3
>REMARK 290 SYMOP SYMMETRY
>REMARK 290 NNNMMM OPERATOR
>REMARK 290 1555 X,Y,Z
>REMARK 290 2555 Z,X,Y
>REMARK 290 3555 Y,Z,X
>CRYST1 40.430 40.430 40.430 80.25 80.25 80.25 R 3 3
>
>
>REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3
>REMARK 290 SYMOP SYMMETRY
>REMARK 290 NNNMMM OPERATOR
>REMARK 290 1555 X,Y,Z
>REMARK 290 2555 -Y,X-Y,Z
>REMARK 290 3555 Y-X,-X,Z
>REMARK 290 4555 X+2/3,Y+1/3,Z+1/3
>REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3
>REMARK 290 6555 Y-X+2/3,-X+1/3,Z+1/3
>REMARK 290 7555 X+1/3,Y+2/3,Z+2/3
>REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3
>REMARK 290 9555 Y-X+1/3,-X+2/3,Z+2/3
>CRYST1 64.520 64.520 32.570 90.00 90.00 120.00 H 3 9

Ibrahim M.Moustafa, Ph.D.
Pennsylvania State University
Biochemistry & Molecular Biology Dept.
201 Althouse Lab.
University Park, PA16802

Tel (814) 863 8703
Fax (814) 865 7927

CCP4bb navigation

CCP4bb <-- 2007 <-- March 2007 <-- 20 March 2007
Previous message:
Subject: Re: coot and stereochemistry
From: Dale Tronrud det102 {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2007-03-20 		Next message:
Subject: ccp4i error on Mac OS
From: Ulrich Genick genick {- at -} BRANDEIS {- dot -} EDU
Date: 2007-03-20


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